Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:38:57 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 275/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
categoryCompare 1.47.0 (landing page) Robert M. Flight
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the categoryCompare package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/categoryCompare.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: categoryCompare |
Version: 1.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings categoryCompare_1.47.0.tar.gz |
StartedAt: 2024-03-02 01:16:21 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 01:23:31 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 430.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: categoryCompare.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings categoryCompare_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/categoryCompare.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘categoryCompare/DESCRIPTION’ ... OK * this is package ‘categoryCompare’ version ‘1.47.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘categoryCompare’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOTERM’ .ccCompareGO: no visible binding for global variable ‘Term’ .cytOutNodes: ... may be used in an incorrect context: exportImage(filename = fileName, type = "png", network = cwObj, ...) .getDesc : <anonymous>: no visible global function definition for ‘Term’ show,HyperGResultCC: no visible global function definition for ‘description’ Undefined global functions or variables: GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM Term description * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ccEnrichResult-class 4.166 0.099 5.048 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/categoryCompare.Rcheck/00check.log’ for details.
categoryCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL categoryCompare ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘categoryCompare’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (categoryCompare)
categoryCompare.Rcheck/categoryCompare-Ex.timings
name | user | system | elapsed | |
GENccEnrichResult-class | 1.067 | 0.035 | 1.312 | |
HyperGParamsCC-class | 0.002 | 0.002 | 0.004 | |
HyperGResultCC-class | 0.002 | 0.002 | 0.004 | |
breakEdges-methods | 1.768 | 0.028 | 2.147 | |
ccCompare | 1.046 | 0.019 | 1.214 | |
ccCompareCollection-class | 0.001 | 0.000 | 0.003 | |
ccCompareResult-class | 0.001 | 0.001 | 0.002 | |
ccData | 1.050 | 0.025 | 1.230 | |
ccEnrich | 1.041 | 0.016 | 1.288 | |
ccEnrichCollection-class | 2.187 | 0.071 | 2.708 | |
ccEnrichResult-class | 4.166 | 0.099 | 5.048 | |
ccGeneList-class | 1.153 | 0.020 | 1.367 | |
ccOptions-class | 0.033 | 0.004 | 0.045 | |
ccOutCyt-methods | 0.001 | 0.001 | 0.001 | |
ccSigList-class | 0.000 | 0.001 | 0.002 | |
cytOutData-methods | 0.001 | 0.001 | 0.001 | |
cytOutNodes-methods | 0.000 | 0.001 | 0.002 | |
hyperGTestCC | 1.626 | 0.048 | 1.940 | |
mergeLists-methods | 1.783 | 0.053 | 2.132 | |
mergedData-class | 1.453 | 0.029 | 1.722 | |
minCount | 3.317 | 0.054 | 3.833 | |
minNodes | 0 | 0 | 0 | |
pvalueType | 2.753 | 0.066 | 3.223 | |
show-methods | 0.000 | 0.001 | 0.001 | |